Domain Model Explains Propagation Dynamics and Stability of Histone H3K27 and H3K36 Methylation Landscapes

Chromatin states must be maintained during cell proliferation to uphold cellular identity and genome integrity. Inheritance of histone modifications is central in this process. However, the histone modification landscape is challenged by incorporation of new unmodified histones during each cell cycle, and the principles governing heritability remain unclear. We take a quantitative computational modeling approach to describe propagation of histone H3K27 and H3K36 methylation states. We measure combinatorial H3K27 and H3K36 methylation patterns by quantitative mass spectrometry on subsequent generations of histones. Using model comparison, we reject active global demethylation and invoke the existence of domains defined by distinct methylation endpoints. We find that H3K27me3 on pre-existing histones stimulates the rate of de novo H3K27me3 establishment, supporting a read-write mechanism in timely chromatin restoration. Finally, we provide a detailed quantitative picture of the mutual antagonism between H3K27 and H3K36 methylation and propose that it stabilizes epigenetic states across cell division. [Display omitted] •Quantitative analysis of K27 and K36 methylation over several histone generations•Computational model invokes the existence of distinct methylation state domains•K27me3 on pre-existing histones stimulates the rate of de novo K27me3 establishment•K27/K36 methylation antagonism enhances stability of epigenetic states Alabert et al. introduce a computational model to describe the propagation of histone K27 and K36 methylations on successive generations of histones. This quantitative model invokes the existence of domains with distinct methylation endpoints and reveals that antagonisms between histone methylations enhance the stability of epigenetic states.